What does the ECU use EGT and CHT sensors for?

EGT's are not used in the leaning program or anything else that I know of.  

Not all of the features of the engine are used.  For instance the "Knock Sensor" is not monitored.

Hopefully a future software update will turn on all the features and use more data to adjust the engine.

It's surprising that it doesn't use a knock sensor if it already has one. What other sensors or features aren't used?

I’m skeptical about the idea that the EGTs don’t affect the ECU. Yesterday I lost an EGT probe just after initial startup.  The Lane A light started flashing and I could see there was no indication on EGT #4.   I did a lane check and it ran poorly when on Lane A only, and better on Lane B only and both.  I know the EGTs only report to Lane A, but if they don’t affect anything why would it run poorly on that lane? I used BUDS to verify the problem and there were no other codes or sensor faults. 

In section 7.5.3 (Fuel Injection Control) of the Rotax 912iS OM the second paragraph states:

“Key input variables are throttle valve position, engine speed signal, intake air temperature, ambient air pressure, manifold pressure, and exhaust temperature”.  

Maybe Lane A incorporates EGT information into the injector mapping, but B does not.  This would make Lane B a good failover for mixture control in the event of an EGT failure affecting Lane A.   Just a guess.   

All I can do is to pass on what I learned from Heavy Maintenance training.  Since then there has not been any software changes so it must still be current.  Eric Tucker et al say EGT's do not control the engine leaning function.

The OM may make mention of the Knock Sensor as well but the fact remains that it is not monitored.

As for the engine running rough (poorly) on lane cycling:  I usually experience the same thing each time I do a run up.  But, when I examine the engine data saved on the Dynon Skyview, nothing changes between the two lanes.  I don't have any current Rotax downloaded data via the dongle so I don't have the ignition timing data.  As I recall from previously looking at that data, ignition timing does change and there is a difference between the timing between the front two cylinders and the rear two cylinders timing.   Ignition timing may change but otherwise EGT's and Fuel Flow are virtually identical between Lane A and Lane B cycling.

Several years ago i had a single EGT failure midway on a flight.  On the way up the EGT was fine.  It failed during run-up on the return flight.  I knew it was the EGT so I returned home.  I left both Lane A and Lane B on for the return flight.

I pulled up the archived engine data from the Dynon display and compared the data (for the first leg with no EGT failure and the second leg with the EGT failure).  Virtually no difference in EGT's, or Fuel flow.  If EGT's were monitored and used in the leaning process, the fuel flow would have been adjusted in an attempt to lower the top of the scale EGT (that failed).

That’s interesting data and seems pretty conclusive in favor of your position.  It just seems like the EGT would be an important data point for mixture control, but I guess manifold pressure and CHT can also tell the story.  Whenever the lane light is flashing it’s easy to think the engine is running rough, so maybe that’s what happened in my case when my EGT probe failed.